1
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Yao J, Hong H. Steric trapping strategy for studying the folding of helical membrane proteins. Methods 2024; 225:1-12. [PMID: 38428472 PMCID: PMC11107808 DOI: 10.1016/j.ymeth.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024] Open
Abstract
Elucidating the folding energy landscape of membrane proteins is essential to the understanding of the proteins' stabilizing forces, folding mechanisms, biogenesis, and quality control. This is not a trivial task because the reversible control of folding is inherently difficult in a lipid bilayer environment. Recently, novel methods have been developed, each of which has a unique strength in investigating specific aspects of membrane protein folding. Among such methods, steric trapping is a versatile strategy allowing a reversible control of membrane protein folding with minimal perturbation of native protein-water and protein-lipid interactions. In a nutshell, steric trapping exploits the coupling of spontaneous denaturation of a doubly biotinylated protein to the simultaneous binding of bulky monovalent streptavidin molecules. This strategy has been evolved to investigate key elements of membrane protein folding such as thermodynamic stability, spontaneous denaturation rates, conformational features of the denatured states, and cooperativity of stabilizing interactions. In this review, we describe the critical methodological advancement, limitation, and outlook of the steric trapping strategy.
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Affiliation(s)
- Jiaqi Yao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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2
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Ortner M, Guschtschin-Schmidt N, Stelzer W, Muhle-Goll C, Langosch D. Permissive Conformations of a Transmembrane Helix Allow Intramembrane Proteolysis by γ-Secretase. J Mol Biol 2023; 435:168218. [PMID: 37536392 DOI: 10.1016/j.jmb.2023.168218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
The intramembrane protease γ-secretase activates important signaling molecules, such as Notch receptors. It is still unclear, however, how different elements within the primary structure of substrate transmembrane domains (TMDs) contribute to their cleavability. Using a newly developed yeast-based cleavage assay, we identified three crucial regions within the TMDs of the paralogs Notch1 and Notch3 by mutational and gain-of-function approaches. The AAAA or AGAV motifs within the N-terminal half of the TMDs were found to confer strong conformational flexibility to these TMD helices, as determined by mutagenesis coupled to deuterium/hydrogen exchange. Crucial amino acids within the C-terminal half may support substrate docking into the catalytic cleft of presenilin, the enzymatic subunit of γ-secretase. Further, residues close to the C-termini of the TMDs may stabilize a tripartite β-sheet in the substrate/enzyme complex. NMR structures reveal different extents of helix bending as well as an ability to adopt widely differing conformational substates, depending on the sequence of the N-terminal half. The difference in cleavability between Notch1 and Notch3 TMDs is jointly determined by the conformational repertoires of the TMD helices and the sequences of the C-terminal half, as suggested by mutagenesis and building molecular models. In sum, cleavability of a γ-secretase substrate is enabled by different functions of cooperating TMD regions, which deepens our mechanistic understanding of substrate/non-substrate discrimination in intramembrane proteolysis.
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Affiliation(s)
- Martin Ortner
- Chair of Biopolymer Chemistry, Technical University of Munich, Freising, Germany
| | - Nadja Guschtschin-Schmidt
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Walter Stelzer
- Chair of Biopolymer Chemistry, Technical University of Munich, Freising, Germany
| | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Dieter Langosch
- Chair of Biopolymer Chemistry, Technical University of Munich, Freising, Germany.
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3
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Cooperation of N- and C-terminal substrate transmembrane domain segments in intramembrane proteolysis by γ-secretase. Commun Biol 2023; 6:177. [PMID: 36792683 PMCID: PMC9931712 DOI: 10.1038/s42003-023-04470-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 01/11/2023] [Indexed: 02/17/2023] Open
Abstract
Intramembrane proteases play a pivotal role in biology and medicine, but how these proteases decode cleavability of a substrate transmembrane (TM) domain remains unclear. Here, we study the role of conformational flexibility of a TM domain, as determined by deuterium/hydrogen exchange, on substrate cleavability by γ-secretase in vitro and in cellulo. By comparing hybrid TMDs based on the natural amyloid precursor protein TM domain and an artificial poly-Leu non-substrate, we find that substrate cleavage requires conformational flexibility within the N-terminal half of the TMD helix (TM-N). Robust cleavability also requires the C-terminal TM sequence (TM-C) containing substrate cleavage sites. Since flexibility of TM-C does not correlate with cleavage efficiency, the role of the TM-C may be defined mainly by its ability to form a cleavage-competent state near the active site, together with parts of presenilin, the enzymatic component of γ-secretase. In sum, cleavability of a γ-secretase substrate appears to depend on cooperating TM domain segments, which deepens our mechanistic understanding of intramembrane proteolysis.
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4
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Van Dinh Q, Liu J, Dutta P. Effect of Slp4-a on Membrane Bending During Prefusion of Vesicles in Blood-Brain Barrier. J Biomech Eng 2023; 145:011006. [PMID: 35838328 PMCID: PMC9445323 DOI: 10.1115/1.4054985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/08/2022] [Indexed: 11/08/2022]
Abstract
Vesicle exocytosis is a promising pathway for brain drug delivery through the blood-brain barrier to treat neurodegenerative diseases. In vesicle exocytosis, the membrane fusion process is initiated by the calcium sensor protein named synaptotagmin-like protein4-a (Slp4-a). Understanding conformational changes of Slp4-a during the prefusion stage of exocytosis will help to develop vesicle-based drug delivery to the brain. In this work, we use molecular dynamics (MD) simulations with a hybrid force field coupling united-atom protein model with MARTINI coarse-grained (CG) solvent to capture the conformational changes of Slp4-a during the prefusion stage. These hybrid coarse-grained simulations are more efficient than all-atom MD simulations and can capture protein interactions and conformational changes. Our simulation results show that the calcium ions play critical roles during the prefusion stage. Only one calcium ion can remain in each calcium-binding pocket of Slp4-a C2 domains. The C2B domain of calcium-unbound Slp4-a remains parallel to the endothelial membrane, while the C2B domain of calcium-bound Slp4-a rotates perpendicular to the endothelial membrane to approach the vesicular membrane. For the calcium-bound case, three Slp4-a proteins can effectively bend lipid membranes at the prefusion stage, which could later trigger lipid stalk between membranes. This work provides a better understanding how C2 domains of Slp4-a operate during vesicle exocytosis from an endothelial cell.
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Affiliation(s)
- Quyen Van Dinh
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920
| | - Jin Liu
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920
| | - Prashanta Dutta
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920
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5
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Baudrexl M, Fida T, Berk B, Schwarz WH, Zverlov VV, Groll M, Liebl W. Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting α-L-Arabinofuranosidase Activity. Front Mol Biosci 2022; 9:907439. [PMID: 35847984 PMCID: PMC9278983 DOI: 10.3389/fmolb.2022.907439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Functional, biochemical, and preliminary structural properties are reported for three glycoside hydrolases of the recently described glycoside hydrolase (GH) family 159. The genes were cloned from the genomic sequences of different Caldicellulosiruptor strains. This study extends the spectrum of functions of GH159 enzymes. The only activity previously reported for GH159 was hydrolytic activity on β-galactofuranosides. Activity screening using a set of para-nitrophenyl (pNP) glycosides suggested additional arabinosidase activity on substrates with arabinosyl residues, which has not been previously reported for members of GH159. Even though the thermophilic enzymes investigated—Cs_Gaf159A, Ch_Gaf159A, and Ck_Gaf159A—cleaved pNP-α-l-arabinofuranoside, they were only weakly active on arabinogalactan, and they did not cleave arabinose from arabinan, arabinoxylan, or gum arabic. However, the enzymes were able to hydrolyze the α-1,3-linkage in different arabinoxylan-derived oligosaccharides (AXOS) with arabinosylated xylose at the non-reducing end (A3X, A2,3XX), suggesting their role in the intracellular hydrolysis of oligosaccharides. Crystallization and structural analysis of the apo form of one of the Caldicellulosiruptor enzymes, Ch_Gaf159A, enabled the elucidation of the first 3D structure of a GH159 member. This work revealed a five-bladed β-propeller structure for GH159 enzymes. The 3D structure and its substrate-binding pocket also provides an explanation at the molecular level for the observed exo-activity of the enzyme. Furthermore, the structural data enabled the prediction of the catalytic amino acids. This was supported by the complete inactivation by mutation of residues D19, D142, and E190 of Ch_Gaf159A.
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Affiliation(s)
- Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Tarik Fida
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Berkay Berk
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | | | - Vladimir V. Zverlov
- Chair of Microbiology, Technical University of Munich, Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Moscow, Russia
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Garching, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
- *Correspondence: Wolfgang Liebl,
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6
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Georgiev DD. Quantum information theoretic approach to the mind–brain problem. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 158:16-32. [DOI: 10.1016/j.pbiomolbio.2020.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 12/25/2022]
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7
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Dhara M, Mantero Martinez M, Makke M, Schwarz Y, Mohrmann R, Bruns D. Synergistic actions of v-SNARE transmembrane domains and membrane-curvature modifying lipids in neurotransmitter release. eLife 2020; 9:e55152. [PMID: 32391794 PMCID: PMC7239655 DOI: 10.7554/elife.55152] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/07/2020] [Indexed: 01/01/2023] Open
Abstract
Vesicle fusion is mediated by assembly of SNARE proteins between opposing membranes. While previous work suggested an active role of SNARE transmembrane domains (TMDs) in promoting membrane merger (Dhara et al., 2016), the underlying mechanism remained elusive. Here, we show that naturally-occurring v-SNARE TMD variants differentially regulate fusion pore dynamics in mouse chromaffin cells, indicating TMD flexibility as a mechanistic determinant that facilitates transmitter release from differentially-sized vesicles. Membrane curvature-promoting phospholipids like lysophosphatidylcholine or oleic acid profoundly alter pore expansion and fully rescue the decelerated fusion kinetics of TMD-rigidifying VAMP2 mutants. Thus, v-SNARE TMDs and phospholipids cooperate in supporting membrane curvature at the fusion pore neck. Oppositely, slowing of pore kinetics by the SNARE-regulator complexin-2 withstands the curvature-driven speeding of fusion, indicating that pore evolution is tightly coupled to progressive SNARE complex formation. Collectively, TMD-mediated support of membrane curvature and SNARE force-generated membrane bending promote fusion pore formation and expansion.
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Affiliation(s)
- Madhurima Dhara
- Institute for Physiology, Center of Integrative Physiology and Molecular Medicine, Saarland UniversityHomburgGermany
| | - Maria Mantero Martinez
- Institute for Physiology, Center of Integrative Physiology and Molecular Medicine, Saarland UniversityHomburgGermany
| | - Mazen Makke
- Institute for Physiology, Center of Integrative Physiology and Molecular Medicine, Saarland UniversityHomburgGermany
| | - Yvonne Schwarz
- Institute for Physiology, Center of Integrative Physiology and Molecular Medicine, Saarland UniversityHomburgGermany
| | - Ralf Mohrmann
- Institute for Physiology, Otto-von-Guericke UniversityMagdeburgGermany
| | - Dieter Bruns
- Institute for Physiology, Center of Integrative Physiology and Molecular Medicine, Saarland UniversityHomburgGermany
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8
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The Metastable XBP1u Transmembrane Domain Defines Determinants for Intramembrane Proteolysis by Signal Peptide Peptidase. Cell Rep 2020; 26:3087-3099.e11. [PMID: 30865896 DOI: 10.1016/j.celrep.2019.02.057] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/07/2018] [Accepted: 02/14/2019] [Indexed: 11/23/2022] Open
Abstract
Unspliced XBP1 mRNA encodes XBP1u, the transcriptionally inert variant of the unfolded protein response (UPR) transcription factor XBP1s. XBP1u targets its mRNA-ribosome-nascent-chain-complex to the endoplasmic reticulum (ER) to facilitate UPR activation and prevents overactivation. Yet, its membrane association is controversial. Here, we use cell-free translocation and cellular assays to define a moderately hydrophobic stretch in XBP1u that is sufficient to mediate insertion into the ER membrane. Mutagenesis of this transmembrane (TM) region reveals residues that facilitate XBP1u turnover by an ER-associated degradation route that is dependent on signal peptide peptidase (SPP). Furthermore, the impact of these mutations on TM helix dynamics was assessed by residue-specific amide exchange kinetics, evaluated by a semi-automated algorithm. Based on our results, we suggest that SPP-catalyzed intramembrane proteolysis of TM helices is not only determined by their conformational flexibility, but also by side-chain interactions near the scissile peptide bond with the enzyme's active site.
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9
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Götz A, Mylonas N, Högel P, Silber M, Heinel H, Menig S, Vogel A, Feyrer H, Huster D, Luy B, Langosch D, Scharnagl C, Muhle-Goll C, Kamp F, Steiner H. Modulating Hinge Flexibility in the APP Transmembrane Domain Alters γ-Secretase Cleavage. Biophys J 2019; 116:2103-2120. [PMID: 31130234 PMCID: PMC6554489 DOI: 10.1016/j.bpj.2019.04.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/14/2019] [Accepted: 04/15/2019] [Indexed: 01/27/2023] Open
Abstract
Intramembrane cleavage of the β-amyloid precursor protein C99 substrate by γ-secretase is implicated in Alzheimer's disease pathogenesis. Biophysical data have suggested that the N-terminal part of the C99 transmembrane domain (TMD) is separated from the C-terminal cleavage domain by a di-glycine hinge. Because the flexibility of this hinge might be critical for γ-secretase cleavage, we mutated one of the glycine residues, G38, to a helix-stabilizing leucine and to a helix-distorting proline. Both mutants impaired γ-secretase cleavage and also altered its cleavage specificity. Circular dichroism, NMR, and backbone amide hydrogen/deuterium exchange measurements as well as molecular dynamics simulations showed that the mutations distinctly altered the intrinsic structural and dynamical properties of the substrate TMD. Although helix destabilization and/or unfolding was not observed at the initial ε-cleavage sites of C99, subtle changes in hinge flexibility were identified that substantially affected helix bending and twisting motions in the entire TMD. These resulted in altered orientation of the distal cleavage domain relative to the N-terminal TMD part. Our data suggest that both enhancing and reducing local helix flexibility of the di-glycine hinge may decrease the occurrence of enzyme-substrate complex conformations required for normal catalysis and that hinge mobility can thus be conducive for productive substrate-enzyme interactions.
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Affiliation(s)
- Alexander Götz
- Physics of Synthetic Biological Systems (E14), Technical University of Munich, Freising, Germany
| | - Nadine Mylonas
- Biomedical Center (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Philipp Högel
- Center for Integrated Protein Science Munich at the Lehrstuhl Chemie der Biopolymere, Technical University Munich, Freising, Germany
| | - Mara Silber
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Hannes Heinel
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Simon Menig
- Physics of Synthetic Biological Systems (E14), Technical University of Munich, Freising, Germany
| | - Alexander Vogel
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Hannes Feyrer
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Dieter Langosch
- Center for Integrated Protein Science Munich at the Lehrstuhl Chemie der Biopolymere, Technical University Munich, Freising, Germany
| | - Christina Scharnagl
- Physics of Synthetic Biological Systems (E14), Technical University of Munich, Freising, Germany.
| | - Claudia Muhle-Goll
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany.
| | - Frits Kamp
- Biomedical Center (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany
| | - Harald Steiner
- Biomedical Center (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
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10
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Götz A, Högel P, Silber M, Chaitoglou I, Luy B, Muhle-Goll C, Scharnagl C, Langosch D. Increased H-Bond Stability Relates to Altered ε-Cleavage Efficiency and Aβ Levels in the I45T Familial Alzheimer's Disease Mutant of APP. Sci Rep 2019; 9:5321. [PMID: 30926830 PMCID: PMC6440955 DOI: 10.1038/s41598-019-41766-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/27/2019] [Indexed: 12/15/2022] Open
Abstract
Cleavage of the amyloid precursor protein's (APP) transmembrane domain (TMD) by γ-secretase is a crucial step in the aetiology of Alzheimer's Disease (AD). Mutations in the APP TMD alter cleavage and lead to familial forms of AD (FAD). The majority of FAD mutations shift the preference of initial cleavage from ε49 to ε48, thus raising the AD-related Aβ42/Aβ40 ratio. The I45T mutation is among the few FAD mutations that do not alter ε-site preference, while it dramatically reduces the efficiency of ε-cleavage. Here, we investigate the impact of the I45T mutation on the backbone dynamics of the substrate TMD. Amide exchange experiments and molecular dynamics simulations in solvent and a lipid bilayer reveal an increased stability of amide hydrogen bonds at the ζ- and γ-cleavage sites. Stiffening of the H-bond network is caused by an additional H-bond between the T45 side chain and the TMD backbone, which alters dynamics within the cleavage domain. In particular, the increased H-bond stability inhibits an upward movement of the ε-sites in the I45T mutant. Thus, an altered presentation of ε-sites to the active site of γ-secretase as a consequence of restricted local flexibility provides a rationale for reduced ε-cleavage efficiency of the I45T mutant.
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Grants
- Deutsche Forschungsgemeinschaft (German Research Foundation)
- Helmholtz-Gemeinschaft (Helmholtz Association)
- Leibniz Supercomputing Centre: Leibniz-Rechenzentrum der Bayerischen Akademie der Wissenschaften, Boltzmannstraße 1, 85748 Garching bei München, Germany, WEB: https://www.lrz.de Gauss Centre for Supercomputing: GCS-Geschäftsstelle Bonn, Ahrstrasse 45, 53175 Bonn, Germany, WEB: http://www.gauss-centre.eu
- Center for Integrated Protein Science: Munich Center For Integrated Protein Science (CIPSM), Butenandtstr. 5 - 13, 81377 Munich, Germany, WEB: http://www.cipsm.de/ Leibniz Supercomputing Centre: Leibniz-Rechenzentrum der Bayerischen Akademie der Wissenschaften, Boltzmannstraße 1, 85748 Garching bei München, Germany, WEB: https://www.lrz.de
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Affiliation(s)
- Alexander Götz
- Lehrstuhl für Physik synthetischer Biosysteme (E14), Technische Universität München, Maximus-von-Imhof Forum 4, 85354, Freising, Germany
| | - Philipp Högel
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Mara Silber
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Iro Chaitoglou
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Claudia Muhle-Goll
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Christina Scharnagl
- Lehrstuhl für Physik synthetischer Biosysteme (E14), Technische Universität München, Maximus-von-Imhof Forum 4, 85354, Freising, Germany.
| | - Dieter Langosch
- Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
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11
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Thermodynamically reversible paths of the first fusion intermediate reveal an important role for membrane anchors of fusion proteins. Proc Natl Acad Sci U S A 2019; 116:2571-2576. [PMID: 30700547 DOI: 10.1073/pnas.1818200116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Biological membrane fusion proceeds via an essential topological transition of the two membranes involved. Known players such as certain lipid species and fusion proteins are generally believed to alter the free energy and thus the rate of the fusion reaction. Quantifying these effects by theory poses a major challenge since the essential reaction intermediates are collective, diffusive and of a molecular length scale. We conducted molecular dynamics simulations in conjunction with a state-of-the-art string method to resolve the minimum free-energy path of the first fusion intermediate state, the so-called stalk. We demonstrate that the isolated transmembrane domains (TMDs) of fusion proteins such as SNARE molecules drastically lower the free energy of both the stalk barrier and metastable stalk, which is not trivially explained by molecular shape arguments. We relate this effect to the local thinning of the membrane (negative hydrophobic mismatch) imposed by the TMDs which favors the nearby presence of the highly bent stalk structure or prestalk dimple. The distance between the membranes is the most crucial determinant of the free energy of the stalk, whereas the free-energy barrier changes only slightly. Surprisingly, fusion enhancing lipids, i.e., lipids with a negative spontaneous curvature, such as PE lipids have little effect on the free energy of the stalk barrier, likely because of its single molecular nature. In contrast, the lipid shape plays a crucial role in overcoming the hydration repulsion between two membranes and thus rather lowers the total work required to form a stalk.
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12
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Scheidt HA, Kolocaj K, Veje Kristensen J, Huster D, Langosch D. Transmembrane Helix Induces Membrane Fusion through Lipid Binding and Splay. J Phys Chem Lett 2018; 9:3181-3186. [PMID: 29799756 DOI: 10.1021/acs.jpclett.8b00859] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The fusion of biological membranes may require splayed lipids whose tails transiently visit the headgroup region of the bilayer, a scenario suggested by molecular dynamics simulations. Here, we examined the lipid splay hypothesis experimentally by relating liposome fusion and lipid splay induced by model transmembrane domains (TMDs). Our results reveal that a conformationally flexible transmembrane helix promotes outer leaflet mixing and lipid splay more strongly than a conformationally rigid one. The lipid dependence of basal as well as of TMD-driven lipid mixing and splay suggests that the cone-shaped phosphatidylethanolamine stimulates basal fusion via enhancing lipid splay and that the negatively charged phosphatidylserine inhibits fusion via electrostatic repulsion. Phosphatidylserine also strongly differentiates basal and helix-driven fusion, which is related to its preferred interaction with the conformationally more flexible transmembrane helix. Thus, the contribution of a transmembrane helix to membrane fusion appears to depend on lipid binding, which results in lipid splay.
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Affiliation(s)
- Holger A Scheidt
- Institute for Medical Physics and Biophysics , Leipzig University , Härtelstrasse 16-18 , 04107 Leipzig , Germany
| | - Katja Kolocaj
- Lehrstuhl für Chemie der Biopolymere , Technische Universität München , Weihenstephaner Berg 3 , 85354 Freising , Germany
- Munich Center For Integrated Protein Science (CIPSM) , Butenandtstrasse 5 , 81377 München , Germany
| | - Julie Veje Kristensen
- Lehrstuhl für Chemie der Biopolymere , Technische Universität München , Weihenstephaner Berg 3 , 85354 Freising , Germany
- Munich Center For Integrated Protein Science (CIPSM) , Butenandtstrasse 5 , 81377 München , Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics , Leipzig University , Härtelstrasse 16-18 , 04107 Leipzig , Germany
| | - Dieter Langosch
- Lehrstuhl für Chemie der Biopolymere , Technische Universität München , Weihenstephaner Berg 3 , 85354 Freising , Germany
- Munich Center For Integrated Protein Science (CIPSM) , Butenandtstrasse 5 , 81377 München , Germany
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13
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Högel P, Götz A, Kuhne F, Ebert M, Stelzer W, Rand KD, Scharnagl C, Langosch D. Glycine Perturbs Local and Global Conformational Flexibility of a Transmembrane Helix. Biochemistry 2018; 57:1326-1337. [DOI: 10.1021/acs.biochem.7b01197] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Philipp Högel
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Alexander Götz
- Physics
of Synthetic Biological Systems (E14), Technical University of Munich, Maximus-von-Imhof Forum 4, 85354 Freising, Germany
| | - Felix Kuhne
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Maximilian Ebert
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Walter Stelzer
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Christina Scharnagl
- Physics
of Synthetic Biological Systems (E14), Technical University of Munich, Maximus-von-Imhof Forum 4, 85354 Freising, Germany
| | - Dieter Langosch
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
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14
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Hastoy B, Clark A, Rorsman P, Lang J. Fusion pore in exocytosis: More than an exit gate? A β-cell perspective. Cell Calcium 2017; 68:45-61. [PMID: 29129207 DOI: 10.1016/j.ceca.2017.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/17/2017] [Accepted: 10/24/2017] [Indexed: 12/14/2022]
Abstract
Secretory vesicle exocytosis is a fundamental biological event and the process by which hormones (like insulin) are released into the blood. Considerable progress has been made in understanding this precisely orchestrated sequence of events from secretory vesicle docked at the cell membrane, hemifusion, to the opening of a membrane fusion pore. The exact biophysical and physiological regulation of these events implies a close interaction between membrane proteins and lipids in a confined space and constrained geometry to ensure appropriate delivery of cargo. We consider some of the still open questions such as the nature of the initiation of the fusion pore, the structure and the role of the Soluble N-ethylmaleimide-sensitive-factor Attachment protein REceptor (SNARE) transmembrane domains and their influence on the dynamics and regulation of exocytosis. We discuss how the membrane composition and protein-lipid interactions influence the likelihood of the nascent fusion pore forming. We relate these factors to the hypothesis that fusion pore expansion could be affected in type-2 diabetes via changes in disease-related gene transcription and alterations in the circulating lipid profile. Detailed characterisation of the dynamics of the fusion pore in vitro will contribute to understanding the larger issue of insulin secretory defects in diabetes.
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Affiliation(s)
- Benoit Hastoy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK.
| | - Anne Clark
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - Patrik Rorsman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK; Metabolic Research, Institute of Neuroscience and Physiology, University of Goteborg, Medicinaregatan 11, S-41309 Göteborg, Sweden
| | - Jochen Lang
- Laboratoire de Chimie et Biologie des Membranes et Nano-objets (CBMN), CNRS UMR 5248, Université de Bordeaux, Allée de Geoffrey St Hilaire, 33600 Pessac, France.
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15
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Wu Z, Thiyagarajan S, O'Shaughnessy B, Karatekin E. Regulation of Exocytotic Fusion Pores by SNARE Protein Transmembrane Domains. Front Mol Neurosci 2017; 10:315. [PMID: 29066949 PMCID: PMC5641348 DOI: 10.3389/fnmol.2017.00315] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/19/2017] [Indexed: 12/26/2022] Open
Abstract
Calcium-triggered exocytotic release of neurotransmitters and hormones from neurons and neuroendocrine cells underlies neuronal communication, motor activity and endocrine functions. The core of the neuronal exocytotic machinery is composed of soluble N-ethyl maleimide sensitive factor attachment protein receptors (SNAREs). Formation of complexes between vesicle-attached v- and plasma-membrane anchored t-SNAREs in a highly regulated fashion brings the membranes into close apposition. Small, soluble proteins called Complexins (Cpx) and calcium-sensing Synaptotagmins cooperate to block fusion at low resting calcium concentrations, but trigger release upon calcium increase. A growing body of evidence suggests that the transmembrane domains (TMDs) of SNARE proteins play important roles in regulating the processes of fusion and release, but the mechanisms involved are only starting to be uncovered. Here we review recent evidence that SNARE TMDs exert influence by regulating the dynamics of the fusion pore, the initial aqueous connection between the vesicular lumen and the extracellular space. Even after the fusion pore is established, hormone release by neuroendocrine cells is tightly controlled, and the same may be true of neurotransmitter release by neurons. The dynamics of the fusion pore can regulate the kinetics of cargo release and the net amount released, and can determine the mode of vesicle recycling. Manipulations of SNARE TMDs were found to affect fusion pore properties profoundly, both during exocytosis and in biochemical reconstitutions. To explain these effects, TMD flexibility, and interactions among TMDs or between TMDs and lipids have been invoked. Exocytosis has provided the best setting in which to unravel the underlying mechanisms, being unique among membrane fusion reactions in that single fusion pores can be probed using high-resolution methods. An important role will likely be played by methods that can probe single fusion pores in a biochemically defined setting which have recently become available. Finally, computer simulations are valuable mechanistic tools because they have the power to access small length scales and very short times that are experimentally inaccessible.
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Affiliation(s)
- Zhenyong Wu
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, CT, United States.,Nanobiology Institute, Yale University, West Haven, CT, United States
| | | | - Ben O'Shaughnessy
- Department of Chemical Engineering, Columbia University, New York, NY, United States
| | - Erdem Karatekin
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, CT, United States.,Nanobiology Institute, Yale University, West Haven, CT, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.,Laboratoire de Neurophotonique, Université Paris Descartes, Faculté des Sciences Fondamentales et Biomédicales, Centre National de la Recherche Scientifique (CNRS), Paris, France
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16
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Yang Z, Gou L, Chen S, Li N, Zhang S, Zhang L. Membrane Fusion Involved in Neurotransmission: Glimpse from Electron Microscope and Molecular Simulation. Front Mol Neurosci 2017. [PMID: 28638320 PMCID: PMC5461332 DOI: 10.3389/fnmol.2017.00168] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Membrane fusion is one of the most fundamental physiological processes in eukaryotes for triggering the fusion of lipid and content, as well as the neurotransmission. However, the architecture features of neurotransmitter release machinery and interdependent mechanism of synaptic membrane fusion have not been extensively studied. This review article expounds the neuronal membrane fusion processes, discusses the fundamental steps in all fusion reactions (membrane aggregation, membrane association, lipid rearrangement and lipid and content mixing) and the probable mechanism coupling to the delivery of neurotransmitters. Subsequently, this work summarizes the research on the fusion process in synaptic transmission, using electron microscopy (EM) and molecular simulation approaches. Finally, we propose the future outlook for more exciting applications of membrane fusion involved in synaptic transmission, with the aid of stochastic optical reconstruction microscopy (STORM), cryo-EM (cryo-EM), and molecular simulations.
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Affiliation(s)
- Zhiwei Yang
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China.,Department of Applied Chemistry, Xi'an Jiaotong UniversityXi'an, China.,School of Life Science and Technology, Xi'an Jiaotong UniversityXi'an, China
| | - Lu Gou
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China
| | - Shuyu Chen
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China
| | - Na Li
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China
| | - Shengli Zhang
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China
| | - Lei Zhang
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China
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17
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Han J, Pluhackova K, Böckmann RA. The Multifaceted Role of SNARE Proteins in Membrane Fusion. Front Physiol 2017; 8:5. [PMID: 28163686 PMCID: PMC5247469 DOI: 10.3389/fphys.2017.00005] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/04/2017] [Indexed: 12/28/2022] Open
Abstract
Membrane fusion is a key process in all living organisms that contributes to a variety of biological processes including viral infection, cell fertilization, as well as intracellular transport, and neurotransmitter release. In particular, the various membrane-enclosed compartments in eukaryotic cells need to exchange their contents and communicate across membranes. Efficient and controllable fusion of biological membranes is known to be driven by cooperative action of SNARE proteins, which constitute the central components of the eukaryotic fusion machinery responsible for fusion of synaptic vesicles with the plasma membrane. During exocytosis, vesicle-associated v-SNARE (synaptobrevin) and target cell-associated t-SNAREs (syntaxin and SNAP-25) assemble into a core trans-SNARE complex. This complex plays a versatile role at various stages of exocytosis ranging from the priming to fusion pore formation and expansion, finally resulting in the release or exchange of the vesicle content. This review summarizes current knowledge on the intricate molecular mechanisms underlying exocytosis triggered and catalyzed by SNARE proteins. Particular attention is given to the function of the peptidic SNARE membrane anchors and the role of SNARE-lipid interactions in fusion. Moreover, the regulatory mechanisms by synaptic auxiliary proteins in SNARE-driven membrane fusion are briefly outlined.
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Affiliation(s)
- Jing Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science CenterXi'an, China; Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-NürnbergErlangen, Germany
| | - Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg Erlangen, Germany
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18
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Stelzer W, Scharnagl C, Leurs U, Rand KD, Langosch D. The Impact of the ‘Austrian’ Mutation of the Amyloid Precursor Protein Transmembrane Helix is Communicated to the Hinge Region. ChemistrySelect 2016. [DOI: 10.1002/slct.201601090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Walter Stelzer
- Lehrstuhl Chemie der Biopolymere; Technical University of Munich and Munich Center for Integrated Protein Science (CIPS ); Weihenstephaner Berg 3 85354 Freising Germany
| | - Christina Scharnagl
- Fakultät für Physik E14; Technical University of Munich; Maximus-von-Imhof-Forum 4 85354 Freising Germany
| | - Ulrike Leurs
- Department of Pharmacy; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Kasper D. Rand
- Department of Pharmacy; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Dieter Langosch
- Lehrstuhl Chemie der Biopolymere; Technical University of Munich and Munich Center for Integrated Protein Science (CIPS ); Weihenstephaner Berg 3 85354 Freising Germany
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19
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Dhara M, Yarzagaray A, Makke M, Schindeldecker B, Schwarz Y, Shaaban A, Sharma S, Böckmann RA, Lindau M, Mohrmann R, Bruns D. v-SNARE transmembrane domains function as catalysts for vesicle fusion. eLife 2016; 5:e17571. [PMID: 27343350 PMCID: PMC4972536 DOI: 10.7554/elife.17571] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/24/2016] [Indexed: 12/22/2022] Open
Abstract
Vesicle fusion is mediated by an assembly of SNARE proteins between opposing membranes, but it is unknown whether transmembrane domains (TMDs) of SNARE proteins serve mechanistic functions that go beyond passive anchoring of the force-generating SNAREpin to the fusing membranes. Here, we show that conformational flexibility of synaptobrevin-2 TMD is essential for efficient Ca(2+)-triggered exocytosis and actively promotes membrane fusion as well as fusion pore expansion. Specifically, the introduction of helix-stabilizing leucine residues within the TMD region spanning the vesicle's outer leaflet strongly impairs exocytosis and decelerates fusion pore dilation. In contrast, increasing the number of helix-destabilizing, ß-branched valine or isoleucine residues within the TMD restores normal secretion but accelerates fusion pore expansion beyond the rate found for the wildtype protein. These observations provide evidence that the synaptobrevin-2 TMD catalyzes the fusion process by its structural flexibility, actively setting the pace of fusion pore expansion.
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Affiliation(s)
- Madhurima Dhara
- Institute for Physiology, Saarland University, Homburg, Germany
| | | | - Mazen Makke
- Institute for Physiology, Saarland University, Homburg, Germany
| | | | - Yvonne Schwarz
- Institute for Physiology, Saarland University, Homburg, Germany
| | - Ahmed Shaaban
- Zentrum für Human- und Molekularbiologie, Saarland University, Homburg, Germany
| | - Satyan Sharma
- Group Nanoscale Cell Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University, Erlangen, Germany
| | - Manfred Lindau
- Group Nanoscale Cell Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ralf Mohrmann
- Zentrum für Human- und Molekularbiologie, Saarland University, Homburg, Germany
| | - Dieter Bruns
- Institute for Physiology, Saarland University, Homburg, Germany
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20
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Scharnagl C, Pester O, Hornburg P, Hornburg D, Götz A, Langosch D. Side-chain to main-chain hydrogen bonding controls the intrinsic backbone dynamics of the amyloid precursor protein transmembrane helix. Biophys J 2014; 106:1318-26. [PMID: 24655507 DOI: 10.1016/j.bpj.2014.02.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 01/28/2014] [Accepted: 02/07/2014] [Indexed: 01/19/2023] Open
Abstract
Many transmembrane helices contain serine and/or threonine residues whose side chains form intrahelical H-bonds with upstream carbonyl oxygens. Here, we investigated the impact of threonine side-chain/main-chain backbonding on the backbone dynamics of the amyloid precursor protein transmembrane helix. This helix consists of a N-terminal dimerization region and a C-terminal cleavage region, which is processed by γ-secretase to a series of products. Threonine mutations within this transmembrane helix are known to alter the cleavage pattern, which can lead to early-onset Alzheimer's disease. Circular dichroism spectroscopy and amide exchange experiments of synthetic transmembrane domain peptides reveal that mutating threonine enhances the flexibility of this helix. Molecular dynamics simulations show that the mutations reduce intrahelical amide H-bonding and H-bond lifetimes. In addition, the removal of side-chain/main-chain backbonding distorts the helix, which alters bending and rotation at a diglycine hinge connecting the dimerization and cleavage regions. We propose that the backbone dynamics of the substrate profoundly affects the way by which the substrate is presented to the catalytic site within the enzyme. Changing this conformational flexibility may thus change the pattern of proteolytic processing.
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Affiliation(s)
| | - Oxana Pester
- Munich Center for Integrated Protein Science (CIPS(M)) at Lehrstuhl Chemie der Biopolymere, Technische Universität München, Freising, Germany
| | - Philipp Hornburg
- Fakultät für Physik E14, Technische Universität München, Freising, Germany
| | - Daniel Hornburg
- Fakultät für Physik E14, Technische Universität München, Freising, Germany
| | - Alexander Götz
- Munich Center for Integrated Protein Science (CIPS(M)) at Lehrstuhl Chemie der Biopolymere, Technische Universität München, Freising, Germany
| | - Dieter Langosch
- Munich Center for Integrated Protein Science (CIPS(M)) at Lehrstuhl Chemie der Biopolymere, Technische Universität München, Freising, Germany
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21
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Dunkelberger EB, Woys AM, Zanni MT. 2D IR cross peaks reveal hydrogen-deuterium exchange with single residue specificity. J Phys Chem B 2013; 117:15297-305. [PMID: 23659731 PMCID: PMC3812256 DOI: 10.1021/jp402942s] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A form of chemical exchange, hydrogen-deuterium exchange (HDX), has long been used as a method for studying the secondary and tertiary structure of peptides and proteins using mass spectrometry and NMR spectroscopy. Using two-dimensional infrared (2D IR) spectroscopy, we resolve cross peaks between the amide II band and a (13)C(18)O isotope-labeled amide I band, which we show measures HDX with site-specific resolution. By rapidly scanning 2D IR spectra using mid-IR pulse shaping, we monitor the kinetics of HDX exchange on-the-fly. For the antimicrobial peptide ovispirin bound to membrane bilayers, we find that the amide II peak decays with a biexponential with rate constants of 0.54 ± 0.02 and 0.12 ± 0.01 min(-1), which is a measure of the overall HDX in the peptide. The cross peaks between Ile-10-labeled ovispirin and the amide II mode, which specifically monitor HDX kinetics at Ile-10, decay with a single rate constant of 0.36 ± 0.1 min(-1). Comparing this exchange rate to theoretically determined exchange rates of Ile-10 for ovispirin in a solution random coil configuration, the exchange rate at Ile-10 is at least 100 times slower, consistent with the known α-helix structure of ovispirin in bilayers. Because backbone isotope labels produce only a very small shift of the amide II band, site-specific HDX cannot be measured with FTIR spectroscopy, which is why 2D IR spectroscopy is needed for these measurements.
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Affiliation(s)
| | - Ann Marie Woys
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706-1396
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706-1396
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22
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The Cleavage Domain of the Amyloid Precursor Protein Transmembrane Helix Does Not Exhibit Above-Average Backbone Dynamics. Chembiochem 2013; 14:1943-8. [DOI: 10.1002/cbic.201300322] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Indexed: 11/07/2022]
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23
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Langer M, Sah R, Veser A, Gütlich M, Langosch D. Structural properties of model phosphatidylcholine flippases. ACTA ACUST UNITED AC 2013; 20:63-72. [PMID: 23352140 DOI: 10.1016/j.chembiol.2012.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/13/2012] [Accepted: 11/20/2012] [Indexed: 11/28/2022]
Abstract
Lipid translocation from one lipid bilayer leaflet to the other, termed flip-flop, is required for the distribution of newly synthesized phospholipids during membrane biogenesis. However, a dedicated biogenic lipid flippase has not yet been identified. Here, we show that the efficiency by which model transmembrane peptides facilitate flip of reporter lipids with different headgroups critically depends on their content of helix-destabilizing residues, the charge state of polar flanking residues, and the composition of the host membrane. In particular, increased backbone dynamics of the transmembrane helix relates to its increased ability to flip lipids with phosphatidylcholine and phosphatidylserine headgroups, whereas a more rigid helix favors phosphatidylethanolamine flip. Further, the transmembrane domains of many SNARE protein subtypes share essential features with the dynamic model peptides. Indeed, recombinant SNAREs possess significant lipid flippase activity.
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Affiliation(s)
- Marcella Langer
- Lehrstuhl für Chemie der Biopolymere, Department für biowissenschaftliche Grundlagen, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising and Munich Center For Integrated Protein Science (CIPS(M)), Germany
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24
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Pester O, Barrett PJ, Hornburg D, Hornburg P, Pröbstle R, Widmaier S, Kutzner C, Dürrbaum M, Kapurniotu A, Sanders CR, Scharnagl C, Langosch D. The backbone dynamics of the amyloid precursor protein transmembrane helix provides a rationale for the sequential cleavage mechanism of γ-secretase. J Am Chem Soc 2013; 135:1317-29. [PMID: 23265086 PMCID: PMC3560327 DOI: 10.1021/ja3112093] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The etiology of Alzheimer's disease depends on the relative abundance of different amyloid-β (Aβ) peptide species. These peptides are produced by sequential proteolytic cleavage within the transmembrane helix of the 99 residue C-terminal fragment of the amyloid precursor protein (C99) by the intramembrane protease γ-secretase. Intramembrane proteolysis is thought to require local unfolding of the substrate helix, which has been proposed to be cleaved as a homodimer. Here, we investigated the backbone dynamics of the substrate helix. Amide exchange experiments of monomeric recombinant C99 and of synthetic transmembrane domain peptides reveal that the N-terminal Gly-rich homodimerization domain exchanges much faster than the C-terminal cleavage region. MD simulations corroborate the differential backbone dynamics, indicate a bending motion at a diglycine motif connecting dimerization and cleavage regions, and detect significantly different H-bond stabilities at the initial cleavage sites. Our results are consistent with the following hypotheses about cleavage of the substrate: First, the GlyGly hinge may precisely position the substrate within γ-secretase such that its catalytic center must start proteolysis at the known initial cleavage sites. Second, the ratio of cleavage products formed by subsequent sequential proteolysis could be influenced by differential extents of solvation and by the stabilities of H-bonds at alternate initial sites. Third, the flexibility of the Gly-rich domain may facilitate substrate movement within the enzyme during sequential proteolysis. Fourth, dimerization may affect substrate processing by decreasing the dynamics of the dimerization region and by increasing that of the C-terminal part of the cleavage region.
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Affiliation(s)
- Oxana Pester
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Paul J. Barrett
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee USA 37232-8725
| | - Daniel Hornburg
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Philipp Hornburg
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Rasmus Pröbstle
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Simon Widmaier
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Christoph Kutzner
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Milena Dürrbaum
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Aphrodite Kapurniotu
- Fachgebiet Peptidbiochemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Charles R. Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee USA 37232-8725
| | - Christina Scharnagl
- Fakultät für Physik E14, Technische Universität München, Maximus-von-Imhof-Forum 4, 85354 Freising, Germany
| | - Dieter Langosch
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
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25
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Stelzer W, Langosch D. Sequence-dependent backbone dynamics of a viral fusogen transmembrane helix. Protein Sci 2012; 21:1097-102. [PMID: 22593029 DOI: 10.1002/pro.2094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 05/09/2012] [Accepted: 05/10/2012] [Indexed: 12/11/2022]
Abstract
The transmembrane domains of membrane fusogenic proteins are known to contribute to lipid bilayer mixing as indicated by mutational studies and functional reconstitution of peptide mimics. Here, we demonstrate that mutations of a GxxxG motif or of Ile residues, that were previously shown to compromise the fusogenicity of the Vesicular Stomatitis virus G-protein transmembrane helix, reduce its backbone dynamics as determined by deuterium/hydrogen-exchange kinetics. Thus, the backbone dynamics of these helices may be linked to their fusogenicity which is consistent with the known over-representation of Gly and Ile in viral fusogen transmembrane helices. The transmembrane domains of membrane fusogenic proteins are known to contribute to lipid bilayer mixing. Our present results demonstrate that mutations of certain residues, that were previously shown to compromise the fusogenicity of the Vesicular Stomatitis virus G-protein transmembrane helix, reduce its backbone dynamics. Thus, the data suggest a relationship between sequence, backbone dynamics, and fusogenicity of transmembrane segments of viral fusogenic proteins.
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Affiliation(s)
- Walter Stelzer
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising and Munich Center for Integrated Protein Science, Freising, Germany
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26
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Ramakrishnan NA, Drescher MJ, Drescher DG. The SNARE complex in neuronal and sensory cells. Mol Cell Neurosci 2012; 50:58-69. [PMID: 22498053 PMCID: PMC3570063 DOI: 10.1016/j.mcn.2012.03.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 03/23/2012] [Accepted: 03/26/2012] [Indexed: 11/28/2022] Open
Abstract
Transmitter release at synapses ensures faithful chemical coding of information that is transmitted in the sub-second time frame. The brain, the central unit of information processing, depends upon fast communication for decision making. Neuronal and neurosensory cells are equipped with the molecular machinery that responds reliably, and with high fidelity, to external stimuli. However, neuronal cells differ markedly from neurosensory cells in their signal transmission at synapses. The main difference rests in how the synaptic complex is organized, with active zones in neuronal cells and ribbon synapses in sensory cells (such as photoreceptors and hair cells). In exocytosis/neurosecretion, SNAREs (soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors) and associated proteins play a critical role in vesicle docking, priming, fusion and synchronization of neurotransmitter release. Recent studies suggest differences between neuronal and sensory cells with respect to the molecular components of their synaptic complexes. In this review, we will cover current findings on neuronal and sensory-cell SNARE proteins and their modulators. We will also briefly discuss recent investigations on how deficits in the expression of SNARE proteins in humans impair function in brain and sense organs.
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Affiliation(s)
| | - Marian J. Drescher
- Department of Otolaryngology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Dennis G. Drescher
- Department of Otolaryngology, Wayne State University School of Medicine, Detroit, MI, USA
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
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27
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Pan Y, Ruan X, Valvano MA, Konermann L. Validation of membrane protein topology models by oxidative labeling and mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:889-898. [PMID: 22410873 DOI: 10.1007/s13361-012-0342-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 01/12/2012] [Accepted: 01/17/2012] [Indexed: 05/31/2023]
Abstract
Computer-assisted topology predictions are widely used to build low-resolution structural models of integral membrane proteins (IMPs). Experimental validation of these models by traditional methods is labor intensive and requires modifications that might alter the IMP native conformation. This work employs oxidative labeling coupled with mass spectrometry (MS) as a validation tool for computer-generated topology models. ·OH exposure introduces oxidative modifications in solvent-accessible regions, whereas buried segments (e.g., transmembrane helices) are non-oxidizable. The Escherichia coli protein WaaL (O-antigen ligase) is predicted to have 12 transmembrane helices and a large extramembrane domain (Pérez et al., Mol. Microbiol. 2008, 70, 1424). Tryptic digestion and LC-MS/MS were used to map the oxidative labeling behavior of WaaL. Met and Cys exhibit high intrinsic reactivities with ·OH, making them sensitive probes for solvent accessibility assays. Overall, the oxidation pattern of these residues is consistent with the originally proposed WaaL topology. One residue (M151), however, undergoes partial oxidation despite being predicted to reside within a transmembrane helix. Using an improved computer algorithm, a slightly modified topology model was generated that places M151 closer to the membrane interface. On the basis of the labeling data, it is concluded that the refined model more accurately reflects the actual topology of WaaL. We propose that the combination of oxidative labeling and MS represents a useful strategy for assessing the accuracy of IMP topology predictions, supplementing data obtained in traditional biochemical assays. In the future, it might be possible to incorporate oxidative labeling data directly as constraints in topology prediction algorithms.
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Affiliation(s)
- Yan Pan
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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Beyond anchoring: the expanding role of the hendra virus fusion protein transmembrane domain in protein folding, stability, and function. J Virol 2012; 86:3003-13. [PMID: 22238302 DOI: 10.1128/jvi.05762-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
While work with viral fusion proteins has demonstrated that the transmembrane domain (TMD) can affect protein folding, stability, and membrane fusion promotion, the mechanism(s) remains poorly understood. TMDs could play a role in fusion promotion through direct TMD-TMD interactions, and we have recently shown that isolated TMDs from three paramyxovirus fusion (F) proteins interact as trimers using sedimentation equilibrium (SE) analysis (E. C. Smith, et al., submitted for publication). Immediately N-terminal to the TMD is heptad repeat B (HRB), which plays critical roles in fusion. Interestingly, addition of HRB decreased the stability of the trimeric TMD-TMD interactions. This result, combined with previous findings that HRB forms a trimeric coiled coil in the prefusion form of the whole protein though HRB peptides fail to stably associate in isolation, suggests that the trimeric TMD-TMD interactions work in concert with elements in the F ectodomain head to stabilize a weak HRB interaction. Thus, changes in TMD-TMD interactions could be important in regulating F triggering and refolding. Alanine insertions between the TMD and HRB demonstrated that spacing between these two regions is important for protein stability while not affecting TMD-TMD interactions. Additional mutagenesis of the C-terminal end of the TMD suggests that β-branched residues within the TMD play a role in membrane fusion, potentially through modulation of TMD-TMD interactions. Our results support a model whereby the C-terminal end of the Hendra virus F TMD is an important regulator of TMD-TMD interactions and show that these interactions help hold HRB in place prior to the triggering of membrane fusion.
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González-Rubio P, Gautier R, Etchebest C, Fuchs PF. Amphipathic-Lipid-Packing-Sensor interactions with lipids assessed by atomistic molecular dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2119-27. [DOI: 10.1016/j.bbamem.2011.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 05/03/2011] [Accepted: 05/04/2011] [Indexed: 12/16/2022]
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Neumann S, Langosch D. Conserved conformational dynamics of membrane fusion protein transmembrane domains and flanking regions indicated by sequence statistics. Proteins 2011; 79:2418-27. [DOI: 10.1002/prot.23063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 03/26/2011] [Accepted: 04/19/2011] [Indexed: 11/07/2022]
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Chalmers MJ, Busby SA, Pascal BD, West GM, Griffin PR. Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions. Expert Rev Proteomics 2011; 8:43-59. [PMID: 21329427 DOI: 10.1586/epr.10.109] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Functional regulation of ligand-activated receptors is driven by alterations in the conformational dynamics of the protein upon ligand binding. Differential hydrogen/deuterium exchange (HDX) coupled with mass spectrometry has emerged as a rapid and sensitive approach for characterization of perturbations in conformational dynamics of proteins following ligand binding. While this technique is sensitive to detecting ligand interactions and alterations in receptor dynamics, it also can provide important mechanistic insights into ligand regulation. For example, HDX has been used to determine a novel mechanism of ligand activation of the nuclear receptor peroxisome proliferator activated receptor-γ, perform detailed analyses of binding modes of ligands within the ligand-binding pocket of two estrogen receptor isoforms, providing insight into selectivity, and helped classify different types of estrogen receptor-α ligands by correlating their pharmacology with the way they interact with the receptor based solely on hierarchical clustering of receptor HDX signatures. Beyond small-molecule-receptor interactions, this technique has also been applied to study protein-protein complexes, such as mapping antibody-antigen interactions. In this article, we summarize the current state of the differential HDX approaches and the future outlook. We summarize how HDX analysis of protein-ligand interactions has had an impact on biology and drug discovery.
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Affiliation(s)
- Michael J Chalmers
- The Scripps Research Molecular Screening Center, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
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32
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Is lipid flippase activity of SNARE transmembrane domains required for membrane fusion? FEBS Lett 2011; 585:1021-4. [PMID: 21362418 DOI: 10.1016/j.febslet.2011.02.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 02/23/2011] [Accepted: 02/23/2011] [Indexed: 11/22/2022]
Abstract
It has been suggested that lipids translocate between the outer and inner leaflets of fusing membranes, or flip-flop, to facilitate changes in bilayer leaflet areas at various stages of fusion. Here, we investigated the lipid flip activity of synthetic peptides that mimic SNARE transmembrane domains (TMDs). These peptides indeed induce flip of marker lipids. However, mutations that reduce flip activity do not diminish fusogenicity and cholesterol blocks flip much more efficiently than fusion. Therefore, our data do not support a role for flip in membrane fusion. On the other hand, the ability of SNARE TMDs to catalyze flip is consistent with a role of SNAREs in biogenic lipid flip.
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Helix-destabilizing, beta-branched, and polar residues in the baboon reovirus p15 transmembrane domain influence the modularity of FAST proteins. J Virol 2011; 85:4707-19. [PMID: 21367887 DOI: 10.1128/jvi.02223-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The fusogenic reoviruses induce syncytium formation using the fusion-associated small transmembrane (FAST) proteins. A recent study indicated the p14 FAST protein transmembrane domain (TMD) can be functionally replaced by the TMDs of the other FAST proteins but not by heterologous TMDs, suggesting that the FAST protein TMDs are modular fusion units. We now show that the p15 FAST protein is also a modular fusogen, as indicated by the functional replacement of the p15 ectodomain with the corresponding domain from the p14 FAST protein. Paradoxically, the p15 TMD is not interchangeable with the TMDs of the other FAST proteins, implying that unique attributes of the p15 TMD are required when this fusion module is functioning in the context of the p15 ecto- and/or endodomain. A series of point substitutions, truncations, and reextensions were created in the p15 TMD to define features that are specific to the functioning of the p15 TMD. Removal of only one or two residues from the N terminus or four residues from the C terminus of the p15 TMD eliminated membrane fusion activity, and there was a direct correlation between the fusion-promoting function of the p15 TMD and the presence of N-terminal, hydrophobic β-branched residues. Substitution of the glycine residues and triserine motif present in the p15 TMD also impaired or eliminated the fusion-promoting activity of the p15 TMD. The ability of the p15 TMD to function in an ecto- and endodomain-specific context is therefore influenced by stringent sequence requirements that reflect the importance of TMD polar residues and helix-destabilizing residues.
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Residue-specific side-chain packing determines the backbone dynamics of transmembrane model helices. Biophys J 2011; 99:2541-9. [PMID: 20959095 DOI: 10.1016/j.bpj.2010.08.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 07/06/2010] [Accepted: 08/12/2010] [Indexed: 12/28/2022] Open
Abstract
The transmembrane domains (TMDs) of membrane-fusogenic proteins contain an overabundance of β-branched residues. In a previous effort to systematically study the relation among valine content, fusogenicity, and helix dynamics, we developed model TMDs that we termed LV-peptides. The content and position of valine in LV-peptides determine their fusogenicity and backbone dynamics, as shown experimentally. Here, we analyze their conformational dynamics and the underlying molecular forces using molecular-dynamics simulations. Our study reveals that backbone dynamics is correlated with the efficiency of side-chain to side-chain van der Waals packing between consecutive turns of the helix. Leu side chains rapidly interconvert between two rotameric states, thus favoring contacts to its i±3 and i±4 neighbors. Stereochemical restraints acting on valine side chains in the α-helix force both β-substituents into an orientation where i,i±3 interactions are less favorable than i,i±4 interactions, thus inducing a local packing deficiency at VV3 motifs. We provide a quantitative molecular model to explain the relationship among chain connectivity, side-chain mobility, and backbone flexibility. We expect that this mechanism also defines the backbone flexibility of natural TMDs.
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Poschner BC, Fischer K, Herrmann JR, Hofmann MW, Langosch D. Structural features of fusogenic model transmembrane domains that differentially regulate inner and outer leaflet mixing in membrane fusion. Mol Membr Biol 2010; 27:1-10. [PMID: 19939203 DOI: 10.3109/09687680903362044] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The transmembrane domains of fusion proteins are known to be important for their fusogenic activity. In an effort to systematically investigate the structure/function relationships of transmembrane domains we had previously designed LV-peptides that mimic natural fusion protein TMDs in their ability to drive fusion after incorporation into liposomal membranes. Here, we investigate the impact of different structural features of LV-peptide TMDs on inner and outer leaflet mixing. We find that fusion driven by the helical peptides involves a hemifusion intermediate as previously seen for natural fusion proteins. Helix backbone dynamics enhances fusion by selectively promoting outer leaflet mixing. Furthermore, the hydrophobic length of the peptides as well as covalent attachment of long acyl chains affects outer and inner leaflet mixing to different extents. Different structural features of transmembrane domains thus appear to differentially influence the rearrangements of lipids in fusion initiation and the hemifusion-to-fusion transition. The relevance of these findings in respect to the function of natural fusion proteins is discussed.
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Affiliation(s)
- Bernhard C Poschner
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center for Integrated Protein Science (CIPSM), Germany
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36
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Pan Y, Konermann L. Membrane protein structural insights from chemical labeling and mass spectrometry. Analyst 2010; 135:1191-200. [DOI: 10.1039/b924805f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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37
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Pan Y, Brown L, Konermann L. Mapping the Structure of an Integral Membrane Protein under Semi-Denaturing Conditions by Laser-Induced Oxidative Labeling and Mass Spectrometry. J Mol Biol 2009; 394:968-81. [DOI: 10.1016/j.jmb.2009.09.063] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 09/28/2009] [Accepted: 09/28/2009] [Indexed: 12/23/2022]
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38
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Poschner BC, Langosch D. Stabilization of conformationally dynamic helices by covalently attached acyl chains. Protein Sci 2009; 18:1801-5. [PMID: 19569191 DOI: 10.1002/pro.155] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Acylation of proteins is known to mediate membrane attachment and to influence subcellular sorting. Here, we report that acylation can stabilize secondary structure. Circular dichroism spectroscopy showed that N-terminal attachment of acyl chains decreases the ability of an intrinsically flexible hydrophobic model peptide to refold from an alpha-helical state to beta-sheet in response to changing solvent conditions. Acylation also stabilized the membrane-embedded alpha-helix. This increase of global helix stability did not result from decreased local conformational dynamics of the helix backbone as assessed by deuterium/hydrogen-exchange experiments. We concluded that acylation can stabilize the structure of intrinsically dynamic helices and may thus prevent misfolding.
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Affiliation(s)
- Bernhard C Poschner
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, 85354 Freising, Germany
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39
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Kaltashov IA, Bobst CE, Abzalimov RR. H/D exchange and mass spectrometry in the studies of protein conformation and dynamics: is there a need for a top-down approach? Anal Chem 2009; 81:7892-9. [PMID: 19694441 PMCID: PMC2805115 DOI: 10.1021/ac901366n] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hydrogen/deuterium exchange (HDX) combined with mass spectrometry (MS) detection has matured in recent years to become a powerful tool in structural biology and biophysics. Several limitations of this technique can and will be addressed by tapping into the ever expanding arsenal of methods to manipulate ions in the gas phase offered by mass spectrometry.
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Affiliation(s)
- Igor A Kaltashov
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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40
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Reversible transition between α-helix and β-sheet conformation of a transmembrane domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1722-30. [DOI: 10.1016/j.bbamem.2009.05.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 05/16/2009] [Accepted: 05/19/2009] [Indexed: 12/28/2022]
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41
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Langosch D, Arkin IT. Interaction and conformational dynamics of membrane-spanning protein helices. Protein Sci 2009; 18:1343-58. [PMID: 19530249 PMCID: PMC2775205 DOI: 10.1002/pro.154] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 04/19/2009] [Accepted: 04/20/2009] [Indexed: 12/23/2022]
Abstract
Within 1 or 2 decades, the reputation of membrane-spanning alpha-helices has changed dramatically. Once mostly regarded as dull membrane anchors, transmembrane domains are now recognized as major instigators of protein-protein interaction. These interactions may be of exquisite specificity in mediating assembly of stable membrane protein complexes from cognate subunits. Further, they can be reversible and regulatable by external factors to allow for dynamic changes of protein conformation in biological function. Finally, these helices are increasingly regarded as dynamic domains. These domains can move relative to each other in different functional protein conformations. In addition, small-scale backbone fluctuations may affect their function and their impact on surrounding lipid shells. Elucidating the ways by which these intricate structural features are encoded by the amino acid sequences will be a fascinating subject of research for years to come.
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Affiliation(s)
- Dieter Langosch
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany.
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42
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Poschner BC, Quint S, Hofmann MW, Langosch D. Sequence-specific conformational dynamics of model transmembrane domains determines their membrane fusogenic function. J Mol Biol 2009; 386:733-41. [PMID: 19154744 DOI: 10.1016/j.jmb.2008.12.077] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 12/29/2008] [Indexed: 10/21/2022]
Abstract
The transmembrane domains of fusion proteins are known to be functionally important and display an overabundance of helix-destabilizing Ile and Val residues. In an effort to systematically study the relationship of fusogenicity and helix stability, we previously designed LV peptides, a low-complexity model system whose hydrophobic core consists of Leu and Val residues at different ratios. The ability of LV peptides to fuse membranes increases with the content of helix-destabilizing residues. Here, we monitored the kinetics of amide deuterium/hydrogen exchange of LV-peptide helices to probe their conformational dynamics. The kinetics indeed increases strongly with the content of helix-destabilizing residues and is likely to reflect local fluctuations of the helix backbones as all peptides exhibit uncorrelated exchange and contain subpopulations of amide deuterium atoms that exchange with different velocities. Interestingly, helices whose amide deuterium atoms are shifted from slower to faster subpopulations are more fusogenic. Novel peptide variants in which Val residues are concentrated at peripheral or central domains of the hydrophobic core were designed to map functionally relevant helix subdomains. Their structural and functional analysis suggests that dynamic domains close to the helix termini are more relevant for fusogenicity than central domains but cooperate with the latter to achieve strong fusogenicity.
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Affiliation(s)
- Bernhard C Poschner
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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43
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Weigang LMM, Langosch D, Letzel T. Gas-phase behavior of noncovalent transmembrane segment complexes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:4089-4097. [PMID: 19025888 DOI: 10.1002/rcm.3843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Specific helix oligomerization between transmembrane segments (TMSs) is often promoted by motifs like GxxxG. Disruption of this motif in the transmembrane segments of vesicular stomatitis virus G-protein and of glycophorin A results in a reduced dimerization level studied by in vivo systems like ToxR. This paper reports the influence of sequence motifs like GxxxG in solution and the gas phase.The transmembrane segments may behave differently in the gas and liquid phase, because of the absence of surrounding solvent molecules in the gas phase. Comparison of experiments depending on peptide properties performed in the gas and liquid phase discloses that the peptides retain 'some memory' of their liquid-phase structure in the gas phase. A direct correlation has been found between helicity in solution as determined by circular dichroism and dimerization in the gas phase monitored by electrospray mass spectrometry. These results show that a proper folding in solution is required for oligomerization.On the other hand, sequence-specific oligomerization depending on the GxxxG motif was not observed with the mass spectrometric detection. Further on, neither concentration-dependent complex studies nor studies regarding complex stability in the gas phase - via collision-induced dissociation (CID) - led to sequence-specific differences.Finally, the findings show that in mass spectrometric measurements noncovalent interactions of studied TMSs is rather more dependent on the secondary structure and proper folding than on their primary structure.
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Affiliation(s)
- Linda M M Weigang
- Lehrstuhl für Chemie der Biopolymere, Department für Biowissenschaftliche Grundlagen, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising - Weihenstephan, Germany
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